TMCC3

protein-coding

transmembrane and coiled-coil domain family 3, the group of MicroRNA protein coding host genes|Transmembrane and coiled-coil domain containing

Gene summary

Enables 14-3-3 protein binding activity and identical protein binding activity. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_020698.4

Inheritance

—

ClinVar variants

U:79B:5

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr12:94,567,122-94,650,557

External References & Databases

Ensembl (ENSG00000057704)

Transcript & Mutation Effects

hg38 • Region Span ~83.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TMCC3 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 75

not providedTotal: 3

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Myoepithelial tumorTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020698.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	3 clinvar	1 clinvar	6
missense			75 clinvar		1 clinvar	76
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	79	3	2	84

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020698.4	RefSeq	NP_065749.3	4	MANE Select
ENST00000261226.9	Ensembl	ENSP00000261226.4	4	MANE Select
NM_001301036.2	RefSeq	NP_001287965.1	3	Standard
ENST00000548918.1	Ensembl	ENSP00000450078.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000261226
Coding exons: 4
Length: 83439
Individuals with no LoFs: 125712
Homozygous LoFs: 0
Heterozygous LoFs: 35
Defined: 125747
p: 0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.923	231	274	0.843	0.0000163	3113
Missense (PolyPhen)		102	135.49	0.75284		1592
Synonymous	0.302	113	117	0.965	0.00000783	914
Loss of Function	1.70	10	17.7	0.564	0.00000105	207

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.00023	0.00023	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.785
RVIS EVS: 0.18
RVIS percentile EVS: 66.13

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.163

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium